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- PDB-2jpn: Solution Structure of T4 Bacteriophage Helicase Uvsw.1 -

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Basic information

Entry
Database: PDB / ID: 2jpn
TitleSolution Structure of T4 Bacteriophage Helicase Uvsw.1
ComponentsATP-dependent DNA helicase uvsW
KeywordsHYDROLASE / uvsw / bacteriophage helicase
Function / homology
Function and homology information


helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Uncharacterised protein UvsW.1 / UvsW.1 domain / DNA helicase UvsW superfamily / : / : / UvsW.1 domain / DNA helicase UvsW, N-terminal / Monooxygenase / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit ...Uncharacterised protein UvsW.1 / UvsW.1 domain / DNA helicase UvsW superfamily / : / : / UvsW.1 domain / DNA helicase UvsW, N-terminal / Monooxygenase / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
ATP-dependent DNA helicase uvsW
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsSivakolundu, S.G. / Lee, T. / White, S.W. / Kriwacki, R.W.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystallographic and NMR Analyses of UvsW and UvsW.1 from Bacteriophage T4
Authors: Kerr, I.D. / Sivakolundu, S. / Li, Z. / Buchsbaum, J.C. / Knox, L.A. / Kriwacki, R. / White, S.W.
History
DepositionMay 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA helicase uvsW


Theoretical massNumber of molelcules
Total (without water)9,0961
Polymers9,0961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ATP-dependent DNA helicase uvsW / Dar protein


Mass: 9096.041 Da / Num. of mol.: 1 / Fragment: sequence database residues, 512-587
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: uvsW, dar / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P20703, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D C(CO)NH
1813D H(CCO)NH
1913D (H)CCH-COSY
11013D 1H-13C NOESY
11113D 1H-15N NOESY
11213D (H)CCH-TOCSY
11312D 1H-15N HSQC, Steady state {1H}-15N NOE

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Sample preparation

DetailsContents: 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 1.66 mM / Component: UvsW.1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.02 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
Felix2000Accelrys Software Inc.processing
Felix2000Accelrys Software Inc.peak picking
Felix2000Accelrys Software Inc.chemical shift assignment
ARIA1.2Linge, O'Donoghue and Nilgeschemical shift assignment
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
TALOSCornilescu, Delaglio and Baxrestraint generation
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
Details: ARIA 1.2 was used to calculate 100 structures. AMBER 9 was used to refine 20 low energy structures using GBSA solvation method.
NMR constraintsNOE constraints total: 1967 / NOE intraresidue total count: 669 / NOE long range total count: 222 / NOE medium range total count: 578 / NOE sequential total count: 498 / Protein phi angle constraints total count: 49 / Protein psi angle constraints total count: 49
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0.73 ° / Maximum upper distance constraint violation: 0.41 Å
Torsion angle constraint violation method: Amber Modeling Package

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